EXPRORER: Rational Cosolvent Set Construction Method for Cosolvent Molecular Dynamics Using Large-Scale Computation

Cosolvent molecular dynamics (CMD) simulations involve an MD simulation of a protein in the presence of explicit water molecules mixed with cosolvent molecules to perform hotspot detection, binding site identification, and binding energy estimation, while other existing methods (e.g., MixMD, SILCS, and MDmix) utilize small molecules that represent functional groups of compounds. However, the cosolvent selections employed in these methods differ and there are only a few cosolvents that are commonly used in these methods. In this study, we proposed a systematic method for constructing a set of cosolvents for drug discovery, termed the EXtended PRObes set construction by REpresentative Retrieval (EXPRORER). First, we extracted typical substructures from FDA-approved drugs, generated 138 cosolvent structures, and for each cosolvent molecule, we conducted CMD simulations to generate a spatial probability distribution map of cosolvent atoms (PMAP). Analyses of PMAP similarity revealed that a cosolvent pair with a PMAP similarity greater than 0.70–0.75 shared similar structural features. We present a method for the construction of a cosolvent subset that satisfies a similarity threshold for all cosolvents, and we tested the constructed sets for four proteins. To our knowledge, this is the first study to include a systematic proposal for cosolvent set construction, and thus, the EXPRORER cosolvents will provide deeper insights into ligand binding sites of various proteins.共溶剂分子动力学（cosolvent molecular dynamics, CMD）模拟指在显性水分子与共溶剂分子混合的体系中对蛋白质开展分子动力学模拟，用于热点区域检测、结合位点识别与结合能估算；而现有其他方法（如MixMD、SILCS与MDmix）则采用代表化合物官能团的小分子。但上述方法所采用的共溶剂选择方案各不相同，且目前此类方法中常用的共溶剂种类寥寥无几。在本研究中，我们提出了一种面向药物发现的共溶剂集构建系统化方法，命名为基于代表性检索的扩展探针集构建方法（EXtended PRObes set construction by REpresentative Retrieval, EXPRORER）。首先，我们从美国食品药品监督管理局（FDA）批准的药物中提取典型亚结构，生成138种共溶剂分子结构；针对每一种共溶剂分子开展CMD模拟，以生成共溶剂原子空间概率分布图（PMAP）。对PMAP相似度的分析表明，当两种共溶剂的PMAP相似度高于0.70~0.75时，二者具有相似的结构特征。我们提出了一种可针对所有共溶剂设定相似度阈值的共溶剂子集构建方法，并针对四种蛋白质对构建的共溶剂集进行了测试。据我们所知，本研究首次提出了共溶剂集构建的系统化方案，因此EXPRORER共溶剂集将为解析各类蛋白质的配体结合位点提供更深入的认知。